I think it boils down to the fact that even though vampires don't need to breathe, they clearly do at least need to simulate breath to pass as human. Obviously the truth behind the whole deal is that the human actor can't be expected to not breathe during filming but if you think about the logic of the fiction, vampires pass as human for a reason, that being to get close to their victims. If that wasn't the intent then why retain a human form at all? If they didn't want the pretense then they may as well keep the bumpy and fangy look all the time.
With that in mind it makes sense that psychologically all the mannerisms and habits that come with breathing would remain from the vampire's human existence. Like the feeling of being out of breath after running, for example. The reality would be that they actually don't need to breathe anymore heavily than normal but the instinct would be to do so, again as a subconscious part of maintaining their human guise.
Also it obvious that a vampire can intake air when needed. The fact that we have seen vampires blowing out flames and the like shows that they are capable of using their lungs. The only difference is that it's not required for them to stay alive (or undead, if you like).
So when it comes to Spike being "drowned", what are we actually seeing? Given all the other effects of breathing we know a vampire mimics it's very likely that their instinct when having their head pushed under water is to choke. It would never kill them but that doesn't mean it's an experience they find enjoyable. As humans we don't die if we have our heads pushed under water for short periods but it's still not an enjoyable thing to have done to you when it's out of your control.
I just tend to see this as an attempt to unsettle Spike. In no way a danger to him but still a nasty form of torture to shake him up.